[2024-01-24 11:50:49,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference
[2024-01-24 11:50:50,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,988] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,989] [INFO] Running command: gunzip -c /var/lib/cwl/stga50d0b14-8963-4cd6-a913-0e6e101caeaa/GCF_003028855.1_ASM302885v1_genomic.fna.gz | prodigal -d GCF_003028855.1_ASM302885v1_genomic.fna/cds.fna -a GCF_003028855.1_ASM302885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:11,209] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:11,209] [INFO] Task started: HMMsearch
[2024-01-24 11:51:11,209] [INFO] Running command: hmmsearch --tblout GCF_003028855.1_ASM302885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/reference_markers.hmm GCF_003028855.1_ASM302885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:11,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:11,535] [INFO] Found 6/6 markers.
[2024-01-24 11:51:11,591] [INFO] Query marker FASTA was written to GCF_003028855.1_ASM302885v1_genomic.fna/markers.fasta
[2024-01-24 11:51:11,591] [INFO] Task started: Blastn
[2024-01-24 11:51:11,592] [INFO] Running command: blastn -query GCF_003028855.1_ASM302885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/reference_markers.fasta -out GCF_003028855.1_ASM302885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:12,667] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:12,671] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:12,672] [INFO] Target genome list was writen to GCF_003028855.1_ASM302885v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:12,678] [INFO] Task started: fastANI
[2024-01-24 11:51:12,678] [INFO] Running command: fastANI --query /var/lib/cwl/stga50d0b14-8963-4cd6-a913-0e6e101caeaa/GCF_003028855.1_ASM302885v1_genomic.fna.gz --refList GCF_003028855.1_ASM302885v1_genomic.fna/target_genomes.txt --output GCF_003028855.1_ASM302885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:36,141] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:36,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:36,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:36,153] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:36,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:36,154] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	100.0	2112	2112	95	conclusive
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	86.5293	1582	2112	95	below_threshold
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	86.4603	1575	2112	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	86.3152	1503	2112	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	86.1658	1572	2112	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	84.4111	1478	2112	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	84.2705	1303	2112	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	83.7529	1398	2112	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	83.7467	1423	2112	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	83.67	1355	2112	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	81.3973	1065	2112	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.0201	864	2112	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.8507	1018	2112	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.7803	989	2112	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.7497	919	2112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:36,155] [INFO] DFAST Taxonomy check result was written to GCF_003028855.1_ASM302885v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:36,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:36,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:36,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/checkm_data
[2024-01-24 11:51:36,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:36,215] [INFO] Task started: CheckM
[2024-01-24 11:51:36,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003028855.1_ASM302885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003028855.1_ASM302885v1_genomic.fna/checkm_input GCF_003028855.1_ASM302885v1_genomic.fna/checkm_result
[2024-01-24 11:52:41,238] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:41,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,265] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:41,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:41,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003028855.1_ASM302885v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:41,267] [INFO] Task started: Blastn
[2024-01-24 11:52:41,267] [INFO] Running command: blastn -query GCF_003028855.1_ASM302885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fc0adf9-99b5-427d-9740-0523ff7ccfcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003028855.1_ASM302885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:43,354] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:43,359] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:43,360] [INFO] Target genome list was writen to GCF_003028855.1_ASM302885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:43,386] [INFO] Task started: fastANI
[2024-01-24 11:52:43,386] [INFO] Running command: fastANI --query /var/lib/cwl/stga50d0b14-8963-4cd6-a913-0e6e101caeaa/GCF_003028855.1_ASM302885v1_genomic.fna.gz --refList GCF_003028855.1_ASM302885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003028855.1_ASM302885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:01,710] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:01,723] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:01,723] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003028855.1	s__Pseudoduganella armeniaca	100.0	2112	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008011715.1	s__Pseudoduganella haloabium	92.1634	1787	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_004421005.1	s__Pseudoduganella plicata	86.5298	1584	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009720835.1	s__Pseudoduganella buxea	86.2506	1512	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002454505.1	s__Pseudoduganella sp002454505	84.55	1223	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830495.1	s__Pseudoduganella flava	84.3957	1481	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009727155.1	s__Pseudoduganella dura	83.8056	1412	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004322755.1	s__Pseudoduganella albidiflava	83.7619	1421	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192225.1	s__Pseudoduganella umbonata	83.6458	1358	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001191005.1	s__Pseudoduganella sp001191005	82.0273	1139	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:01,725] [INFO] GTDB search result was written to GCF_003028855.1_ASM302885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:01,726] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:01,729] [INFO] DFAST_QC result json was written to GCF_003028855.1_ASM302885v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:01,729] [INFO] DFAST_QC completed!
[2024-01-24 11:53:01,729] [INFO] Total running time: 0h2m12s